## Reasons for omitting loci:
## 1 - Marker has fewer than 2 alleles representing substitutions
## 2 - Required homozygous individuals for the 2 most frequent alleles are not present
## 3 - The second most frequent allele is found only in one heterozygous individual
## 4 - Dataset is invariant for the most frequent allele
## 5 - Dataset is invariant for the allele listed as the first ALT in the vcf input
CHROM	POS	QUAL	REASON